It always comes down to this, the nubbins of the project where the parts are scattered about as you try to fix what's wrong and realize that you've screwed it up so bad that it will never be put together right again.
Let's jump back a step. I decided that the metastory should be continuous, with illuminating backstory thrown in as needed. I pulled out the one third of the narrative that contained the crucial scenes and rewrote/edited them as a single story. That went well. It was when i tried to stick the backstory parts into this framework that the trouble began. Parts no longer fit where they were before, the chronology suddenly turned wonky, and, and, and, . . . I despair of ever getting this together again, it is so screwed up. This has happened before and is probably a consequence of something my mind is working on but has not yet resolved.
The first thing I tried was putting everything back into a simple chronological sequence which failed again because all the important action comes at the end of a LOT of backstory. FAIL!
The next effort was to cull the story, a difficult task since I have an insane loyalty to my WAW (Words-already-written). Nevertheless I began the process of carving away any WAW that didn't support the main thesis. The result was a pretty bland story but lots of action and hardly any backstory at all. FAIL!
Frustrated I restored the full draft and once again turned to my faithful copy of Tobias's Twenty Master Plots to see if there is some approach that would stand a chance of success. As usual, I learned only that I had missed no opportunity insofar as plot points, but the story still lacked a pleasing structure. What to do next? What haven't I thought of?
Rather than beat my brains against this wall of blocks I decided to go back to work on a hard SF novella with the hope that working on something completely different would clarify my mind. As these things happen, a new approach popped into my head no sooner than I got into the rhythm of the new piece. Resisting the impulse to jump back I simply made a few notes, put them aside, and continued working on the novella.
It is so nice to think you are in control of the process.